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Remove sample identities from the repository; document the rule

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Datasets may be confidential; sample names and measured unit cells committed to
the repo can leak outside the group working on them. Scrub existing occurrences
and add a "No sample identities in the repository" section to CLAUDE.md
(forbidden: sample/dataset names, internal codes, measured cells tied to a
sample; fine: space group / lattice / twinning descriptors).

- Comments: replace internal dataset codes and protein names with the
  crystallographic situation they illustrate (centred vs pseudo-symmetric,
  holohedral, cubic, F-cubic/hexagonal, ...).
- Docs: same, in the analysis/writer/stream references and example configs.
- Tests: rename sample-named identifiers, TEST_CASE names, file prefixes and
  asserted labels to neutral crystallographic names (e.g. tetragonal_uc);
  behaviour unchanged. Reduce the CrystFEL reference PDB to a bare CRYST1 cell
  file (cell.pdb) and rename the reference data file.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-07-15 17:19:43 +02:00
co-authored by Claude Opus 4.8
parent 0f3ccda779
commit abbee2d4dc
27 changed files with 159 additions and 4079 deletions
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tests/DiffractionExperimentTest.cpp
+2 -2
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@@ -365,8 +365,8 @@ TEST_CASE("DiffractionExperiment_SampleName", "[DiffractionExperiment]") {
REQUIRE_NOTHROW(x.SampleName(""));
REQUIRE(x.GetSampleName().empty());
REQUIRE_NOTHROW(x.SampleName("lyso1"));
REQUIRE(x.GetSampleName() == "lyso1");
REQUIRE_NOTHROW(x.SampleName("test_sample"));
REQUIRE(x.GetSampleName() == "test_sample");
}
TEST_CASE("DiffractionExperiment_SaveCalibration", "[DiffractionExperiment]") {